Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2278
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 29444
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.34
Found at i:4305 original size:15 final size:15
Alignment explanation
Indices: 4287--4356 Score: 61
Period size: 15 Copynumber: 4.5 Consensus size: 15
4277 CATTATTCGC
*
4287 TTTATATTTATAGTA
1 TTTATATTTATAATA
*
4302 TTTATATATATTTAATA
1 TTTATAT-T-TATAATA
* *
4319 ATTATATTTAAAATA
1 TTTATATTTATAATA
4334 TTATATATTTATAA-A
1 TT-TATATTTATAATA
*
4349 ATTATATT
1 TTTATATT
4357 CATTAAATAA
Statistics
Matches: 44, Mismatches: 8, Indels: 7
0.75 0.14 0.12
Matches are distributed among these distances:
14 6 0.14
15 15 0.34
16 12 0.27
17 11 0.25
ACGTcount: A:0.43, C:0.00, G:0.01, T:0.56
Consensus pattern (15 bp):
TTTATATTTATAATA
Found at i:4323 original size:17 final size:19
Alignment explanation
Indices: 4289--4325 Score: 51
Period size: 17 Copynumber: 2.1 Consensus size: 19
4279 TTATTCGCTT
*
4289 TATATTTATAGTATTTATA
1 TATATTTATAGTAATTATA
4308 TATATTTA-A-TAATTATA
1 TATATTTATAGTAATTATA
4325 T
1 T
4326 TTAAAATATT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
17 8 0.47
18 1 0.06
19 8 0.47
ACGTcount: A:0.41, C:0.00, G:0.03, T:0.57
Consensus pattern (19 bp):
TATATTTATAGTAATTATA
Found at i:4338 original size:14 final size:13
Alignment explanation
Indices: 4308--4356 Score: 53
Period size: 13 Copynumber: 3.5 Consensus size: 13
4298 AGTATTTATA
*
4308 TATATTTAATAAT
1 TATATTTAAAAAT
4321 TATATTTAAAATATT
1 TATATTTAAAA-A-T
4336 ATATATTTATAAAAT
1 -TATATTTA-AAAAT
4351 TATATT
1 TATATT
4357 CATTAAATAA
Statistics
Matches: 31, Mismatches: 1, Indels: 7
0.79 0.03 0.18
Matches are distributed among these distances:
13 10 0.32
14 7 0.23
15 2 0.06
16 9 0.29
17 3 0.10
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (13 bp):
TATATTTAAAAAT
Found at i:4342 original size:16 final size:16
Alignment explanation
Indices: 4321--4355 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
4311 ATTTAATAAT
4321 TATATTTA-AAATATTA
1 TATATTTATAAA-ATTA
4337 TATATTTATAAAATTA
1 TATATTTATAAAATTA
4353 TAT
1 TAT
4356 TCATTAAATA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 15 0.83
17 3 0.17
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (16 bp):
TATATTTATAAAATTA
Found at i:4933 original size:147 final size:146
Alignment explanation
Indices: 4762--5062 Score: 539
Period size: 147 Copynumber: 2.1 Consensus size: 146
4752 GCTTGGCTTC
*
4762 TTAATAATGCAGAAAGTACTTTTAACTCTTAAAATTTAAAACATAAATAAATTATTTAAATTTAA
1 TTAATAATGCAGAAAGTACTTTTAACTCTTAAAATTTAAAAAATAAATAAATTATTTAAATTTAA
* *
4827 ATTTGATGCATTAATCATATAATAATAAATTTATTTATATTTATTTTTAAAATTTTTTAATATAA
66 ATTTAATGCATTAATCACAT-ATAATAAATTTATTTATATTTATTTTTAAAATTTTTTAATATAA
*
4892 TGTAATTATTTAATTGA
130 TATAATTATTTAATTGA
4909 TTAATAATGCAGAAAGTACTTTTAACTCTTAAAATTTAAAAAATAAATAAATTATTTAAATTTAA
1 TTAATAATGCAGAAAGTACTTTTAACTCTTAAAATTTAAAAAATAAATAAATTATTTAAATTTAA
* *
4974 ATTTAATGCATTAATCACATATAATAAATTTATTTGTATTTATTTTTAAATTTTTTTAATATAAT
66 ATTTAATGCATTAATCACATATAATAAATTTATTTATATTTATTTTTAAAATTTTTTAATATAAT
5039 ATAATTATTTAATTGA
131 ATAATTATTTAATTGA
5055 TTAATAAT
1 TTAATAAT
5063 ATTTTATATT
Statistics
Matches: 148, Mismatches: 6, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
146 66 0.45
147 82 0.55
ACGTcount: A:0.45, C:0.05, G:0.04, T:0.47
Consensus pattern (146 bp):
TTAATAATGCAGAAAGTACTTTTAACTCTTAAAATTTAAAAAATAAATAAATTATTTAAATTTAA
ATTTAATGCATTAATCACATATAATAAATTTATTTATATTTATTTTTAAAATTTTTTAATATAAT
ATAATTATTTAATTGA
Found at i:8043 original size:132 final size:132
Alignment explanation
Indices: 7806--8064 Score: 455
Period size: 132 Copynumber: 2.0 Consensus size: 132
7796 AATCGAATAC
* * **
7806 TGAAGTTCATTCCCCTAGGCTCCCTGAGATTGGGAAAAAGCTGATATGTGCATCAAATCAGTTTA
1 TGAAGTTCAATCCCCTAGGCTCCCTGAGATTGGGAAAAAGCTGACATGCACATCAAATCAGTTTA
7871 CCAGCTCAAATGACCAGCAGATAGTGAATAGGTCACCTCCCAAAAGGCTTCCAGGTGGTGCTTGC
66 CCAGCTCAAATGACCAGCAGATAGTGAATAGGTCACCTCCCAAAAGGCTTCCAGGTGGTGCTTGC
7936 AT
131 AT
*
7938 TGAAGTTCAATCCCCTAGGCTCCCTGAGATTGGGAAAAAGCTGACATGCATATCAAATCAGTTTA
1 TGAAGTTCAATCCCCTAGGCTCCCTGAGATTGGGAAAAAGCTGACATGCACATCAAATCAGTTTA
* *
8003 CCAGCTCAGATGACCAGCAGATAGTGAATAGTTCACCTCCCAAAAGGCTTCCAGGTGGTGCT
66 CCAGCTCAAATGACCAGCAGATAGTGAATAGGTCACCTCCCAAAAGGCTTCCAGGTGGTGCT
8065 CGAATTTCTC
Statistics
Matches: 120, Mismatches: 7, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
132 120 1.00
ACGTcount: A:0.29, C:0.24, G:0.22, T:0.24
Consensus pattern (132 bp):
TGAAGTTCAATCCCCTAGGCTCCCTGAGATTGGGAAAAAGCTGACATGCACATCAAATCAGTTTA
CCAGCTCAAATGACCAGCAGATAGTGAATAGGTCACCTCCCAAAAGGCTTCCAGGTGGTGCTTGC
AT
Found at i:8246 original size:42 final size:42
Alignment explanation
Indices: 8187--8269 Score: 166
Period size: 42 Copynumber: 2.0 Consensus size: 42
8177 CCAGAAGCAA
8187 TAACAACTCGCAGGAATTAGTACCTTATCAAAGCAGCAGACC
1 TAACAACTCGCAGGAATTAGTACCTTATCAAAGCAGCAGACC
8229 TAACAACTCGCAGGAATTAGTACCTTATCAAAGCAGCAGAC
1 TAACAACTCGCAGGAATTAGTACCTTATCAAAGCAGCAGAC
8270 AAGGGTCGGG
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
42 41 1.00
ACGTcount: A:0.39, C:0.25, G:0.17, T:0.19
Consensus pattern (42 bp):
TAACAACTCGCAGGAATTAGTACCTTATCAAAGCAGCAGACC
Found at i:10728 original size:18 final size:18
Alignment explanation
Indices: 10705--10747 Score: 54
Period size: 18 Copynumber: 2.4 Consensus size: 18
10695 TAGTATTATG
*
10705 TATATTTTGA-CATGTTCA
1 TATATTTT-ATCATATTCA
10723 TATATTTTATCATATTCA
1 TATATTTTATCATATTCA
10741 TAT-TTTT
1 TATATTTT
10748 TTATGTAATT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
17 5 0.22
18 18 0.78
ACGTcount: A:0.28, C:0.09, G:0.05, T:0.58
Consensus pattern (18 bp):
TATATTTTATCATATTCA
Found at i:11039 original size:11 final size:11
Alignment explanation
Indices: 11023--11095 Score: 57
Period size: 11 Copynumber: 7.0 Consensus size: 11
11013 GTTACATTCA
11023 TATATTTATAT
1 TATATTTATAT
11034 TATATTTATAT
1 TATATTTATAT
* *
11045 TATTTTTGTAT
1 TATATTTATAT
* *
11056 T-GAGTTATACT
1 TATATTTATA-T
*
11067 T-TAATTA-AT
1 TATATTTATAT
11076 T-T-TTTATAT
1 TATATTTATAT
11085 TATATTTATAT
1 TATATTTATAT
11096 CGTGTCTCGA
Statistics
Matches: 49, Mismatches: 9, Indels: 8
0.74 0.14 0.12
Matches are distributed among these distances:
8 3 0.06
9 6 0.12
10 6 0.12
11 34 0.69
ACGTcount: A:0.32, C:0.01, G:0.04, T:0.63
Consensus pattern (11 bp):
TATATTTATAT
Found at i:11203 original size:19 final size:18
Alignment explanation
Indices: 11168--11214 Score: 51
Period size: 19 Copynumber: 2.6 Consensus size: 18
11158 TAATTTACAT
*
11168 AAAAT-TTTAAAATATAA
1 AAAATATTTAAAAAATAA
11185 AAAATATTTAAATAAATAA
1 AAAATATTTAAA-AAATAA
* *
11204 TAATTATTTAA
1 AAAATATTTAA
11215 TACGATTTAA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
17 5 0.20
18 6 0.24
19 14 0.56
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (18 bp):
AAAATATTTAAAAAATAA
Found at i:11630 original size:20 final size:21
Alignment explanation
Indices: 11593--11635 Score: 52
Period size: 20 Copynumber: 2.1 Consensus size: 21
11583 ATTATTTTAA
11593 TATTAATATCTATATATT-TT
1 TATTAATATCTATATATTATT
* * *
11613 TATTAATATTTTTTTATTATT
1 TATTAATATCTATATATTATT
11634 TA
1 TA
11636 AATAATAATT
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
20 15 0.79
21 4 0.21
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.65
Consensus pattern (21 bp):
TATTAATATCTATATATTATT
Found at i:12287 original size:32 final size:32
Alignment explanation
Indices: 12247--12334 Score: 124
Period size: 32 Copynumber: 2.8 Consensus size: 32
12237 GACATAATCT
12247 CTCATAAATTTGATTAATATTAAATAAAATTA
1 CTCATAAATTTGATTAATATTAAATAAAATTA
* *
12279 CTCATAAATTTGATAAATATTAAATATAATTA
1 CTCATAAATTTGATTAATATTAAATAAAATTA
* *
12311 CTTATAAATTT-AATAATTATTAAA
1 CTCATAAATTTGATTAA-TATTAAA
12335 AAGTTTCAAC
Statistics
Matches: 50, Mismatches: 5, Indels: 2
0.88 0.09 0.04
Matches are distributed among these distances:
31 3 0.06
32 47 0.94
ACGTcount: A:0.50, C:0.06, G:0.02, T:0.42
Consensus pattern (32 bp):
CTCATAAATTTGATTAATATTAAATAAAATTA
Found at i:12334 original size:16 final size:16
Alignment explanation
Indices: 12283--12334 Score: 52
Period size: 16 Copynumber: 3.2 Consensus size: 16
12273 AAATTACTCA
* *
12283 TAAATTTGATAAATAT
1 TAAATTTAATAATTAT
* *
12299 TAAATATAATTACTTA-
1 TAAATTTAA-TAATTAT
12315 TAAATTTAATAATTAT
1 TAAATTTAATAATTAT
12331 TAAA
1 TAAA
12335 AAGTTTCAAC
Statistics
Matches: 28, Mismatches: 6, Indels: 4
0.74 0.16 0.11
Matches are distributed among these distances:
15 5 0.18
16 19 0.68
17 4 0.14
ACGTcount: A:0.52, C:0.02, G:0.02, T:0.44
Consensus pattern (16 bp):
TAAATTTAATAATTAT
Found at i:13596 original size:20 final size:20
Alignment explanation
Indices: 13571--13609 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
13561 ACTGCATTTC
13571 AAATAAAGAAATAACAAAAT
1 AAATAAAGAAATAACAAAAT
* *
13591 AAATAAATAAATAAGAAAA
1 AAATAAAGAAATAACAAAA
13610 ACATTTCGAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.77, C:0.03, G:0.05, T:0.15
Consensus pattern (20 bp):
AAATAAAGAAATAACAAAAT
Found at i:17277 original size:2 final size:2
Alignment explanation
Indices: 17270--17309 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
17260 TTATATTTCA
17270 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
17310 GATTTAGATA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:18042 original size:22 final size:23
Alignment explanation
Indices: 18014--18057 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 23
18004 TAAACATCAT
18014 CTTTCA-TTCATTCAAGAATACC
1 CTTTCATTTCATTCAAGAATACC
*
18036 CTTTCATTTCTTTCAAGAATAC
1 CTTTCATTTCATTCAAGAATAC
18058 TTGTAAAAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
22 6 0.30
23 14 0.70
ACGTcount: A:0.30, C:0.25, G:0.05, T:0.41
Consensus pattern (23 bp):
CTTTCATTTCATTCAAGAATACC
Found at i:19414 original size:2 final size:2
Alignment explanation
Indices: 19402--19444 Score: 77
Period size: 2 Copynumber: 21.5 Consensus size: 2
19392 GAATATTGAT
*
19402 AC AC GC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC
19444 A
1 A
19445 AAAGAATTTG
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.49, C:0.49, G:0.02, T:0.00
Consensus pattern (2 bp):
AC
Found at i:22311 original size:4 final size:4
Alignment explanation
Indices: 22304--22329 Score: 52
Period size: 4 Copynumber: 6.5 Consensus size: 4
22294 TTATTTTCAG
22304 TACA TACA TACA TACA TACA TACA TA
1 TACA TACA TACA TACA TACA TACA TA
22330 TATATATATA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 22 1.00
ACGTcount: A:0.50, C:0.23, G:0.00, T:0.27
Consensus pattern (4 bp):
TACA
Found at i:23206 original size:62 final size:62
Alignment explanation
Indices: 23084--23204 Score: 181
Period size: 63 Copynumber: 1.9 Consensus size: 62
23074 TCCATCTAAC
* *
23084 ACTTTGTATTGAATCTTTGAAGTTATATAGTCTAATATATAATATACAACCTGTAAAAATAT
1 ACTTAGTATTGAATCTTTGAAGTTATATAATCTAATATATAATATACAACCTGTAAAAATAT
* *
23146 ACTTAGTATTGAATCTTTTTGAAGTTATATAATCT-ATATATTATATACAACCTGGAAAA
1 ACTTAGTATTGAATC--TTTGAAGTTATATAATCTAATATATAATATACAACCTGTAAAA
23205 TAGCGATATA
Statistics
Matches: 53, Mismatches: 4, Indels: 3
0.88 0.07 0.05
Matches are distributed among these distances:
62 14 0.26
63 22 0.42
64 17 0.32
ACGTcount: A:0.40, C:0.10, G:0.10, T:0.40
Consensus pattern (62 bp):
ACTTAGTATTGAATCTTTGAAGTTATATAATCTAATATATAATATACAACCTGTAAAAATAT
Found at i:24760 original size:14 final size:15
Alignment explanation
Indices: 24741--24771 Score: 55
Period size: 14 Copynumber: 2.1 Consensus size: 15
24731 ATTTAAAAAA
24741 ATTAAATATAT-TTT
1 ATTAAATATATATTT
24755 ATTAAATATATATTT
1 ATTAAATATATATTT
24770 AT
1 AT
24772 ATCATATATT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 11 0.69
15 5 0.31
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (15 bp):
ATTAAATATATATTT
Done.